The pan-cancer analysis of whole genomes The expansion of whole-genome sequencing studies from individual ICGC and TCGA working groups presented the opportunity to undertake a meta-analysis of genomic features across tumour types. To achieve this, the PCAWG Consortium was established. A Technical Working Group implemented the informatics analyses by aggregating the raw sequencing data from different working groups that studied individual tumour types, aligning the sequences to the human genome and delivering a set of high-quality somatic mutation calls for downstream analysis (Extended Data Fig. 1). Given the recent meta-analysis

The landscape of genomic alterations across childhood cancers a list of authors and affiliations appears at the end of the paper. OPENPan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7-8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.Cure rates for childhood cancers have increased to about 80% in recent decades, but cancer is still the leading cause of death by disease in the developed world among children over one year of age 1,2 . Furthermore, many children who survive cancer suffer from long-term sequelae of surgery, cytotoxic chemotherapy, and radiotherapy, including mental disabilities, organ toxicities, and secondary cancers 3 . A crucial step in developing more specific and less damaging therapies is the unravelling of the complete genetic repertoire of paediatric malignancies, which differ from adult malignancies in terms of their histopathological entities and molecular subtypes 4 . Over the past few years, many entityspecific sequencing efforts have been launched, but the few paediatric pan-cancer studies thus far have focused only on mutation frequencies, germline predisposition, and alterations in epigenetic regulators [4][5][6] .We have carried out a broad exploration of cancers in children, adolescents, and young adults, by incorporating small mutations and copy-number or structural variants on somatic and germline levels, and by identifying putative cancer genes and comparing them to those previously reported in adult cancers by The Cancer Genome Atlas (TCGA) 7 . We have also examined mutational signatures and potential drug targets. The compendium of genetic alterations presented here is available to the scientific community at http://www.pedpancan.com.This integrative analysis includes 24 types of cancer and covers all major childhood cancer entities, many of which occur exclusively in children 8 (Fig. 1, Supplementary Table 1). Ninety-five per cent of the patients in this study were diagnosed during childhood or adolescence (aged 18 years or younger) and 5% as young adults (up to 25 years) (Extended Data ...

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© F e r r a t a S t o r t i F o u n d a t i o nphomas. In BL the MYC translocation always involves one of the immunoglobulin loci (most commonly IGH, alternatively IGL or IGK) and is considered a disease-initiating event which occurs in the context of a rather simple karyotype. Indeed, the genomic complexity in BL is, overall, low. [6][7][8] In contrast, MYC translocations in other mature Bcell lymphomas frequently involve non-IG partners and are mostly found in complex karyotypes, often in addition to well-known primary aberrations including the IGH-BCL2 translocation.6,9-11 Consequently, they likely occur during disease progression rather than disease initiation. Indeed, in 20-80% of cases of DLBCL and BCLU with a MYC breakpoint, there is an accompanying BCL2 and/or BCL6 breakpoint. [12][13][14][15][16] According to the World Health Organization (WHO) classification, lymphomas in which such a combination of a MYC break with a BCL2 break and/or a BCL6 break (fur- (DHL). 4 All other lymphomas with a MYC breakpoint, irrespective of the presence of other aberrations, are called "single-hit" lymphomas (SHL). MYC breaks are seen in approximately 10% (3-17%) of all DLBCL and 15-20% of FL grade 3B, 17,18 representing on average a DHL in 50-60%. 14,[16][17][18][19][20] This also implies that the remaining 40-50% of MYC + lymphomas are "single-hit" and that their importance, despite this high percentage, might have been underappreciated. These lymphomas with MYC translocations, including DHL, have received increased attention because several studies showed them to run an aggressive clinical course. 9,11,21 However, gene expression and other molecular genetic data are scarce 3,22 and, consequently, the molecular make up of DHL and SHL other than BL remains largely unknown. Moreover, it is unclear in which pathological and molecular aspects DHL differs from SHL other than molecular Burkitt lymphoma (mBL).therIn that respect it should be noted that, in the presence or absence of a MYC break, oncogenes other than BCL2 and BCL6, including BCL3, chromosomal locus 9p13 (potentially affecting PAX5), CCNE1, as well as unknown partners involved in IGH breaks, can be deregulated through juxtaposition to one of the IG-loci. 16,[23][24][25][26] Breakpoints affecting both MYC and these genes might, therefore, also point to a DHL, although according to the WHO classification they are defined as SHL. 4 To investigate differences and similarities between SHL and DHL as well as between BCL2 + /MYC + and BCL6+ /MYC + DHL we explored the morphological, immunohistochemical, genetic and gene expression features of 80 adult MYC + mature aggressive B-cell lymphomas other than mBL. Methods Sample selection and pathology reviewAll lymphomas were investigated as part of the Molecular Mechanisms in Malignant Lymphomas (MMML) network project. The MMML protocols have been approved centrally by the institutional review board of the coordination center in Göttingen, Germany. All cases with an mBL gene expression signature (see Bioinformatica...